i posted this somewhere else too, but i think penny's dad may have assumed control (if he didn't have it all along) of dharma, and that's who's on the freighter off the island. they've come back to mete out vengence upon ben and co. for the massacre of the original dharma island folks. he is very rich, and would presumably be able to fund such an operation. it could also explain why naomi had the picture of desmond and penny on her when she landed. the dharma folks in the boat knew approximately where the island was, but because of the frequency jam, were unable to accurately pinpoint it, so they sent out a search copter with naomi in it.